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    <h1>The tkigraph manual</h1>

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    <p>tkigraph is a basic Graphical User Interface (GUI) to some
      igraph functions. </p>

    <h2>What is tkigraph?</h2>
    
    <p>tkigraph is a simple Graphical User Interface to the igraph R
    package. R is a general purpose programming language and
    environment, used mostly but not exclusively for statistical
    analysis. igraph is an extension package to R. tkigraph lets you
    use some basic features of igraph via a GUI, instead of typing in
    R commands.</p>

    <h2>Installing and starting tkigraph</h2>

    <p>Well, if you are reading these lines, then you probably already
      know how to install and start tkigraph.
      If not, here is how to do it.</p>
    
    <p>First, install the GNU R software package. It can be downloaded
      from <i><a href="http://www.r-project.org">the R website</a></i>, but
      first check your system, because it might be already
      installed. You can also ask your system administrator to
      install it for you.</p>
    
    <p>Second, you need to install the igraph extension
      package. First, start R by clicking on its icon in Windows, or
      by typing "R" into a terminal and pressing ENTER on Linux.
      Now type in
      <pre>
	install.package("igraph")
      </pre>
      and press ENTER. After choosing an appropriate mirror site, R
      downloads and installs the igraph package.
    </p>

    <p>Third, you need to load the igraph package and start
      tkigraph. This can be done by typing
      <pre>
	library(igraph)
	tkigraph()
      </pre>
      (in two separate lines, pressing ENTER after each line) 
      into your R session. You should see a new windows appear, it
      looks like the one on the picture below.</p>
    
    <h2>The tkigraph window</h2>
    
    <p>The main window of tkigraph look like this:</p>

    <p><img alt="Main tkigraph window" src="tkigraph-main.gif"></p>
    
    <p>Almost all the window is occupied by the list of graphs in the
      workspace. Unlike on the picture for you this is initially
      empty. Every graph has a number, in the <code>#</code> column, a
      name that is not necessarily unique, you can change the name of
      the graph to whatever you like. In the last three columns you
      can see the number of vertices and edges in the graph, and
      whether it is directed or not.
    </p>

    <p>In the leftmost column there is a checkbox for every graph, you
      can select one or more graphs using this and then perform
      operations on them. Some operations require exactly one graph to
      be selected, others work happily on many graphs as well. You
      will always get an error message if not the appropriate number
      of graphs were selected for an operation.
    </p>
    
    <h2>The tkigraph menus</h2>

    <p>
      Creating new graphs or performing operations on them can be
      done by selecting entries from the main menu. Let us discuss
      briefly what the various menus are good for.
    </p>

    <h3>Graph menu</h3>
    
    <p>
      The Graph menu lets you create and delete graphs, show them in
      an edge list format, calculate some basic properties for
      them. Moreover all file-related operations are here a well.
    </p>    

    <h3>Draw menu</h3>
    
    <p>
      In this menu you can draw your graphs using various layouts,
      possibly also interactively. There are two entries in the menu.
      The first one (Simple) tries to do the plotting automatically;
      first it chooses an appropriate layout for the graph and then
      tries to guess the graphical parameters to make the plot look
      good. Finally it creates a non-interactive plot.
    </p>

    <p>
      The advanced plotting lets you choose various graphical
      parameters, and you also have the possibility to create an
      interactive plot.
    </p>

    <h3>Centrality menu</h3>

    <p>
      Lets you calculate various degree centrality measures, plus edge
      betweenness. The results are always shown in a table that can be
      sorted according to all of its columns and the data can also be
      exported into a text file.
    </p>

    <h3>Distances menu</h3>

    <p>
      Various measures related to path lengths in the network are
      included in this menu.
    </p>
    
    <h3>Subgraphs menu</h3>

    <p>
      This menu contains three slightly related entries. Components
      are maximal connected subgraphs of a graph. Communities are
      natural modules in the graph, a module is a subgraph that has
      more edges within the module than between the module and the
      rest of the graph. (Loosely speaking.) In the 'Communities' menu
      you can run the Spinglass algorithm by J Reichardt and S
      Bornholdt. Cohesion measures how difficult it is to disconnect a
      graph by removing vertices from it. The last menu entry
      calculates cohesion for all components in the selected graph.
    </p>

    <h3>Motifs menu</h3>

    <p>
      Motifs are small subgraphs with a given structure. The first
      menu entry in this menu just plots all possible motifs of a
      given size in a directed or directed graphs. The second menu
      entry finds all the different motifs in the selected graph and
      plots all the different motifs annotated with the number of
      motifs of that kind found in the graph. It also plots a
      histogram for the various motifs.
    </p>
    
    <h3>Help menu</h3>

    <p>
      This is what you are reading right now.
    </p>

    <h3>Quit</h3>
    
    <p>
      Not really a menu, just a button. Lets you quit from tkigraph.
    </p>

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